title: SKMM1 4 hours (ATAC2) FHD286 2

description: TREATMENT

value: 4 hr

value: 50 nM FHD286


title: Parasrampuria_mRNA_Seq_shHD-33full_nb_2

status: Public on May 01 2024

type: SRA

city: Winston-Salem

first: Keith

middle: T.

last: Gagnon

state: North Carolina

address: 575 Patterson Ave

department: Biochemistry and Molecular Biology

country: USA

institute: Wake Forest University School of Medicine

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_shHD33fullnb.csv

library_source: transcriptomic

data_processing:
Sequenced reads were basecalled and demultiplexed using Dorado (v0.5.1).
Minimap2 alignment software was used to align demultiplexed reads to the GENCODE transcriptome reference Release 45 (GRCh38.p14).
Bam files were quantified using the Salmon RNA transcript quantification.
RNA-Seq data was analyzed using the DESeq2 (v1.42.1) package following the transcript abundance and tximport/tximeta input data format.
DESeq2 analysis codes are available in the supplementary file section.
GENCODE transcriptome reference Release 45 (GRCh38.p14)
Assembly: Parasrampuria_DESeq2_gene_counts.csv: Raw gene counts found using DESeq2 between sequenced samples using genes of interest.
Supplementary files format and content: Parasrampuria_Top_Gene_Change_Summary.csv: Top ten genes differentially expressed determined by greatest p-adj value normlaized to shMCHR control.
Supplementary files format and content: Parasrampuria_DESeq2_results_XXX.csv: DESeq2 results output to .csv with GeneIDs. Gene differentiation normalized to shMCHR control.

molecule: polyA RNA

organism: Homo sapiens

source_name: Coriell Institute HD fibroblasts (GM04281)

growth_protocol: HD fibroblasts were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Gibco), 1x non-essential amino acids (100X, Gibco), and 1% sodium pyruvate (100X, Gibco) at 37°C in 5% CO2.

extract_protocol:
Total RNA was Trizol extracted 7 days following infection and poly-A was isolated using magnetic bead purification methods.
The isolated mRNA was prepared using the cDNA-PCR Barcoding Kit V14 (Oxford Nanopore Technologies) following the manufacturers protocol and sequenced on a PromethION 2 Solo instrument (ONT).
RNA-Seq by cDNA-PCR, short read sequencing by Oxford Nanopore P2 Solo methods

treatment_protocol: Cells were infected with lentivirus vectors encoding smRNA at a MOI of 5 containing 1 ug/mL polybrene and incubated at 37°C in a humidified 5% CO incubator, changing media regularly.

tag: cell line

tag: cell type

value: Fibroblast

tag: biomaterial provider

tag: genotype

value: HTT-Patient

tag: treatment

value: Infection with lentiviral particles encoding smRNA


title: Primed MOI75 iPSC_6 (Methylation)

type: genomic

city: San Francisco

first: Akira

last: Kunitomi

state: CA

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description:
SAMPLE 46
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts

hyb_protocol: The bisulfite conversion of 500 ng genomic DNA was performed using the EZ DNA Methylation Kit (Zymo Research), and the bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K or EPIC BeadChip Kit using standard Illumina protocol

scan_protocol: Using illumina iScan according to recommended scanner setting

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.

extract_protocol: Genomic DNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)

value: Human induced pluripotent stem cells

tag: gender

value: Female


title: SKMM1 4 hours (ATAC2) Trametinib 1

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: TREATMENT

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using BOTWIE2
Peaks were called by an inhouse program
Assembly: hg19
Supplementary files format and content: peak-read counts in wig format

source_name: cell line

growth_protocol: NCIH929 and SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

extract_protocol:
DNA was extracted following the Omni-ATACseq protocol published by Corces MR et al (Nat Methods, 2017).
DNA libraries were prepared for sequencing using standard Illumina protocols (Ceribelli M, et al. Cancer Cell, 2016).

treatment_protocol: The myeloma cell lines NCIH929 and SKMM1 were grown at 0.5 x 10^6 cells/ml and either treated with DMSO, 50 nM FHD286, 50 nM trametinib, or combination (50 nM FHD286 PLUS 50 M trametinib) for 4 hours..  50 000 cells were collected for each sample.

tag: tissue

value: cell line

value: human multiple myeloma

tag: time

value: 50 nM trametinib


title: SKMM1 4 hours (ATAC2) FHD286 1

description: TREATMENT


title: Primed MOI75 iPSC_5 (Methylation)

description:
SAMPLE 45
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI75 iPSC_4 (Methylation)

description:
SAMPLE 44
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: SKMM1 4 hours (ATAC2) DMSO 2

description: CTRL

value: DMSO


title: Parasrampuria_mRNA_Seq_shHD-33full_nb_1

value: Coriell Institute HD fibroblasts (GM04281)


title: Parasrampuria_mRNA_Seq_shHD-33full-mimic_3

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_shHD33fullmimic.csv


title: Primed MOI75 iPSC_3 (Methylation)

description:
SAMPLE 43
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI75 iPSC_2 (Methylation)

description:
SAMPLE 42
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: SKMM1 4 hours (ATAC2) DMSO 1

description: CTRL


title: Parasrampuria_mRNA_Seq_shHD-33full-mimic_2


title: Primed MOI15 iPSC_8 (Methylation)

description:
SAMPLE 40
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: U2OS, pLVX-NAB2-STAT6, control,  3' mRNA-seq, biol rep4

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment: STAR
tag density files: deepTools package was used to generate BigWiggle files
gene counts:  FeatureCounts (Liao et al., 2014)
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization). Tab delimited gene count files were generated with FeatureCounts.

molecule: total RNA

growth_protocol: U2OS cells  were cultured and maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% super calf serum and Glutmax.

extract_protocol:
RNA was extracted using the Zymo RNA Miniprep kitand then used to make sequencing libraries.
QuantSeq 3' - mRNA Seq Library Prep Kit for Illumina (Lexogen)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLVX-Tet-On Advanced (ClonTech) and pLVX-NAB2-STAT6-FLAG-Tight-Puro. U2OS were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours.  After that, cells were selected with 200 ug/ml of Neomycin (Corning, cat#MT30234CR) in fresh medium. Cells were selected in Neomycin for two weeks with fresh media being added 3-4 weeks and cells split 1:3 when reaching 80-90% confluency. Then cells were plated into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of medium fresh lentivirus media generated using pLVX-NAB2-STAT6-FLAG-Tight-Puro with 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G) per well was added to replace the old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, cells were disassociated with Trypsin and plated at a low density in a 15 cm dish.  Single cells were cultured with 0.5 ug/ml of puromycin for the next 2-3 weeks until colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened after addition of 1ug/mL Doxycline by verified by Western Blot. ATAC-seq was done without doxycycline treatment and after 1, 2, and 3 days of 1ug/mL doxycycline treatment.

value: osteosarcoma

value: No treatment


title: Primed MOI15 iPSC_5 (Methylation)

description:
SAMPLE 37
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI15 iPSC_7 (Methylation)

description:
SAMPLE 39
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Parasrampuria_mRNA_Seq_shHD-33full-mimic_1


title: Primed MOI75 iPSC_8 (Methylation)

description:
SAMPLE 48
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI15 iPSC_6 (Methylation)

description:
SAMPLE 38
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Parasrampuria_mRNA_Seq_shHD2.4_3

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_shHD24.csv


title: U2OS, pLVX-NAB2-STAT6, control,  3' mRNA-seq, biol rep2


title: Primed MOI15 iPSC_4 (Methylation)

description:
SAMPLE 36
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI75 iPSC_7 (Methylation)

description:
SAMPLE 47
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Parasrampuria_mRNA_Seq_shHD2.4_2


title: U2OS, pLVX-NAB2-STAT6, control,  3' mRNA-seq, biol rep3


title: Primed MOI15 iPSC_2 (Methylation)

description:
SAMPLE 34
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Primed MOI15 iPSC_1 (Methylation)

description:
SAMPLE 33
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: U2OS, pLVX-NAB2-STAT6, control,  3' mRNA-seq, biol rep1


title: Parasrampuria_mRNA_Seq_shMCHR_3

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv


title: U2OS, pLVX-NAB2-STAT6, 3 days doxycycline,  3' mRNA-seq, biol rep4

value: 3 days 1ug/mL doxycycline


title: U2OS, pLVX-NAB2-STAT6, 3 days doxycycline,  3' mRNA-seq, biol rep3


title: Parasrampuria_mRNA_Seq_shHD2.4_1


title: nmt41Chp2pamcherry

city: Waltham

first: Melissa

last: Seman

address: 415 South St

institute: Brandeis University

data_processing:
The sequences were trimmed with Trimmomatic. Then aligned with BWA. Samtools was used to index and sort the reads. Then bamCoverage was used to make bigwig files using normalization RPKM.
Assembly: Schizosaccharomyces_pombe_all_chromosomes
Supplementary files format and content: bigwig

organism: Schizosaccharomyces pombe

source_name: EMMC media, grown to log phase at 32C, then grown at 18C for 2 hours

extract_protocol:
Cells were lysed with bead beating
ChIP-seq libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. 1 ng of DNA was used as starting material.

treatment_protocol: Cells were resuspended in PBS, crosslinked with 1.5mM EGS for 30 min at 25C followed by 1% formaldehyde for 30min at 25C. Then quenched with 130mM glycine.

tag: chip antibody

value: mCherry


title: untagged_Chp2pamcherry

growth_protocol: EMMC media, grown to log phase at 32C, then grown at 18C for 2 hours

value: WT


title: nmt1Chp2pamcherry

value: EMMC media, grown to log phase at 32C, then grown at 18C for 2 hours


title: nmt81Chp2pamcherry


title: Primed MOI75 iPSC_1 (Methylation)

description:
SAMPLE 41
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: U2OS, pLVX-NAB2-STAT6, 3 days doxycycline,  3' mRNA-seq, biol rep2


title: nmt81Chp2pamcherry_clr4D

value: nmt81-Chp2-pamCherry, clr4D


title: Primed MOI15 iPSC_3 (Methylation)

description:
SAMPLE 35
Primed induced pluripotent stem cells derived from adult human dermal fibroblasts


title: Parasrampuria_mRNA_Seq_shMCHR_1

value: Fibroblast


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline,  3' mRNA-seq, biol rep4

value: 2 days 1ug/mL doxycycline


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline,  3' mRNA-seq, biol rep3


title: h2a.z_27_ZT4

city: Cambridge

first: Anna

last: Brestovitsky

address: Bateman Street

country: United Kingdom

institute: Sainsbury Laboratory (SLCU), University of Cambridge

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: hta8,hta9,hta11 triple mutant seedlings

growth_protocol: Seedlings were grown at 27C in short days for 10 days and collected at 8 time pointes. ZT0 time point just before the lights are on (End of the night); ZT8-just before the light are off(end of the day)

extract_protocol:
Total RNA was isolated from 30 mg of grinded seedlings using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using 1 ug of high-integrity total RNA (RIN>8) using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, cat. No. NEB #E7420). Libraries were sequenced in-house on an Illumina NextGen 500 sequencer using paired-end sequencing of 75 bp in length.

treatment_protocol: Growing in 27C, short days

tag: temperature

tag: time of the day

value: h2a.z triple mutant seedlings


title: h2a.z_27_ZT8


title: h2a.z_27_ZT1


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline,  3' mRNA-seq, biol rep2


title: h2a.z_27_ZT0-4


title: h2a.z_27_ZT12


title: h2a.z_27_ZT0-2


title: h2a.z_27_ZT0


title: h2a.z_27_ZT16


title: Parasrampuria_mRNA_Seq_mock_1

description:
Oxford Nanopore Technologies Promethion 2 Solo
Parasrampuria_DESeq2_gene_counts.csv
Parasrampuria_Top_Gene_Change_Summary.csv
Parasrampuria_DESeq2_results_mock_treatment.csv

value: HTT-Patient

value: Infection with lentiviral particles encoding vector control smRNA


title: Parasrampuria_mRNA_Seq_shMCHR_2

value: Infection with lentiviral particles encoding smRNA


title: HEY_shPQBP1_3

city: Jinan

first: Xihan

last: Liu

state: Shandong

address: Wenhuaxi Road #44

country: China

institute: Shandong University

data_processing:
Thresholds for raw reads filtration were minimum average read quality score=7 and minimum read length=500bp, and ribosomal RNA (rRNA) were discarded.
Full-length, non-chemiric (FLNC) transcripts were obtained after mapping to the hg38 genome with minimap2 (version 2.18) and removing redundant transcripts with cDNA_Cupcake package.
Full length reads were mapped to the reference transcriptome sequence. Reads with match quality above 5 were further used to quantify. Expression levels were estimated by reads per gene/transcript per 10,000 reads mapped.
Differential transcript expression was obtained by DESeq R package (1.18.0). Significant different expression was filtered out by |Fold change| > 2 and p <0.05].
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Count values of trancripts for each Sample

source_name: HEY

extract_protocol:
1 µg total RNA was employed for cDNA library construction according to Oxford Nanopore Technology (ONT) protocol.
Full length mRNAs were reverse transcripted by SuperScript IV First-Strand Synthesis System (Invitrogen) and amplified for 14 circles with LongAmp Tag (NEB). Then PCR products were under FFPE DNA repair and end-repair (NEB) steps and adaptor ligation using T4 DNA ligase (NEB). DNA purification was performed by Agencourt XP beads according to ONT protocol.
Long-read nanopore sequencing

value: HEY

value: ovarian cancer cells

value: PQBP1 knockdown

value: Dox inducement (1 microg/ml)

value: Day 3


title: dek3arp6_27_T8_rep2

source_name: dek3-2/arp6-1 seedlings

growth_protocol: Seedlings were grown at 17c or 27C in short days for 10 days and collected at 2 time pointes. ZT0 time point just before the lights are on (End of the night); ZT8-just before the light are off(end of the day)

treatment_protocol: Growing in 17C or 27C

value: T8 (just before lights turn off)

tag: replicate


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline,  3' mRNA-seq, biol rep1

value: osteosarcoma


title: dek3arp6_27_T0_rep2

value: T0 (just before lights turn on)


title: HEY_shPQBP1_1


title: Parasrampuria_mRNA_Seq_mock_3

value: Coriell Institute HD fibroblasts (GM04281)


title: dek3arp6_17_T8_rep2


title: dek3arp6_17_T8_rep1


title: U2OS, pLVX-NAB2-STAT6, 1 day doxycycline,  3' mRNA-seq, biol rep3

value: 1 day 1ug/mL doxycycline


title: HEY_shPQBP1_2


title: dek3arp6_27_T0_rep1


title: U2OS, pLVX-NAB2-STAT6, 1 day doxycycline,  3' mRNA-seq, biol rep4


title: dek3arp6_17_T0_rep2


title: U2OS, pLVX-NAB2-STAT6, 3 days doxycycline,  3' mRNA-seq, biol rep1

value: 3 days 1ug/mL doxycycline


title: Parasrampuria_mRNA_Seq_mock_2

value: Fibroblast


title: dek3arp6_17_T0_rep1


title: dek3arp6_27_T8_rep1


title: dek3_27_T0_rep2

source_name: dek3-2 seedlings


title: dek3_27_T8_rep2


title: U2OS, pLVX-NAB2-STAT6, control, FLAG, biol rep2

description: NAB2-STAT6 (FLAG) ChIP-seq in U2OS pLVX-NAB2-STAT6 cells in control conditions

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLVX-Tet-On Advanced (ClonTech) and pLVX-NAB2-STAT6-FLAG-Tight-Puro. U2OS were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours.  After that, cells were selected with 200 ug/ml of Neomycin (Corning, cat#MT30234CR) in fresh medium. Cells were selected in Neomycin for two weeks with fresh media being added 3-4 weeks and cells split 1:3 when reaching 80-90% confluency. Then cells were plated into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of medium fresh lentivirus media generated using pLVX-NAB2-STAT6-FLAG-Tight-Puro with 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G) per well was added to replace the old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, cells were disassociated with Trypsin and plated at a low density in a 15 cm dish.  Single cells were cultured with 0.5 ug/ml of puromycin for the next 2-3 weeks until colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened after addition of 1ug/mL Doxycline by verified by Western Blot. ChIP-seq was done without doxycycline treatment and after 2 days of 1ug/mL doxycycline treatment.

value: No treatment

value: M2-Flag (Sigma-Aldrich F1804)


title: U2OS, pLVX-NAB2-STAT6, 1 day doxycycline,  3' mRNA-seq, biol rep2


title: HEY_shNC_1

value: NC


title: dek3_27_T8_rep1


title: U2OS, pLVX-NAB2-STAT6, 1 day doxycycline,  3' mRNA-seq, biol rep1


title: dek3_17_T8_rep1


title: U2OS, pLVX-NAB2-STAT6, control, FLAG, biol rep1


title: dek3_17_T0_rep2


title: siPC2possiMRTFA_4_S20

city: Toronto

first: Andras

last: Kapus

state: Ontario

address: 209 Victoria Street

department: Keenan Research Centre for Biomedical Science

country: Canada

institute: St. Michael's Hospital

data_processing:
FastQC v0.11.8 for quality control assessment and Trimgalore_v0.6.3_dev to eliminate low-quality reads.
A quasi-mapping Salmon 0.14.1 1 was used mapping to the pig reference transcriptome (Ensembl: Sus_scrofa.Sscrofa11.1.cds.all 2023-04-22 ) and with  HISAT2 (Sus scrofa 11.1, http://asia.ensembl.org/Sus_scrofa/Info/Index) aligner using default parameters.
Transcript abundance was  calculated using bioconductor Rsubread package.
Assembly: Sus scrofa 11.1
Supplementary files format and content: LLC-PK1_siPC_count

organism: Sus scrofa

source_name: kidney

growth_protocol: LLC-PK1 porcine proximal tubule cell line were cultured in DMEM, supplemented with 10% FBS and penicillin-streptomycin in humidified environment with 5% CO2 at 37 degree centigrade.

extract_protocol:
Total RNA was isolated with RNeasy® Plus Mini (Qiagen, Venlo, Netherlands), following the manufacturer’s protocol.
mRNA libraries were prepared using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® Ultra™

treatment_protocol: Cells were transfected at 30-40% confluency and with siRNA(siNR, siPC1,siPC2, siPC1 & siMRTFA (aka siPC1siMRTFA), siPC2 & siMRTFA (aka siPC2siMRTFA)  respectively using RNAiMax, following the manufacturer’s protocol.

value: kidney

value: Epithelial cell


title: dek3_17_T8_rep2


title: siPC2possiMRTFA_3_S19

value: LLC-PK1 porcine proximal tubule cell line


title: arp6_27_T8_rep2

source_name: arp6-1 seedlings


title: U2OS, pLVX-NAB2-STAT6, control, EGR1, biol rep2

description: EGR1 ChIP-seq in U2OS pLVX-NAB2-STAT6 cells in control conditions

value: EGR1 (Bethyl A303-390A)


title: arp6_27_T8_rep1


title: siPC2possiMRTFA_2_S18


title: U2OS, pLVX-NAB2-STAT6, control, EGR1, biol rep1


title: siPC2possiMRTFA_1_S17


title: arp6_27_T0_rep1


title: siPC1possiMRTFA_4_S16


title: arp6_17_T8_rep1


title: HEY_shNC_2

value: HEY

value: ovarian cancer cells


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, FLAG, biol rep2

description: NAB2-STAT6 (FLAG) ChIP-seq in U2OS pLVX-NAB2-STAT6 cells after 2 days 1ug/mL doxycycline treatment

value: 2 days 1ug/mL doxycycline


title: arp6_27_T0_rep2


title: arp6_17_T8_rep2

value: T8 (just before lights turn off)


title: dek3_27_T0_rep1


title: HEY_shNC_3

value: Day 3


title: siPC1possiMRTFA_3_S15


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, FLAG, biol rep1

value: osteosarcoma


title: arp6_17_T0_rep1

value: T0 (just before lights turn on)


title: Col_27_T8_rep2

source_name: Col-0 seedlings


title: dek3_17_T0_rep1


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, EGR1, biol rep1

description: EGR1 ChIP-seq in U2OS pLVX-NAB2-STAT6 cells after 2 days 1ug/mL doxycycline treatment


title: arp6_17_T0_rep2


title: Col_27_T8_rep1


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, ATAC, biol rep2

description: ATAC in U2OS pLVX-NAB2-STAT6 cells after 2 days 1ug/mL doxycycline treatment

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment: BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

extract_protocol:
Omni ATAC-seq was performed on both control and 2 days 1ug/mL doxycycline treated U2OS pLVX-NAB2-STAT6 cells according to Corces et al 2017. Briefly, 50,000 cells were washed in  ATAC-resuspension buffer (RSB)  with 0.1% Tween-20 and then lysed by incubated on ice for 3 minutes in RSB with 0.1% NP-40 and 0.1% Tween-20. Lysis was washed out in RSB 0.1% Tween-20 and nuclei was pelleted by centrifugation at 600g/4°C/5 minutes. Nuclei were then incubated in transposition mixture for 30 minutes at 37°C while shaking at 1000rpm. DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014). DNA was then amplified for 5 cycles with ATAC index primers and NEBNext Ultra II Q5 Master Mix (NEB #M0544). Additional amplification cycles were then determined by qPCR using 5uL of original amplification with PerfeCTa SYBR Green FastMix Reaction Mixes (Quantabio 95072-012). After additional amplification cycles with remaining 15uL DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014) and quantified by QUBIT.
Omni-ATAC-seq (Corces et al. 2017)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLVX-Tet-On Advanced (ClonTech) and pLVX-NAB2-STAT6-FLAG-Tight-Puro. U2OS were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours.  After that, cells were selected with 200 ug/ml of Neomycin (Corning, cat#MT30234CR) in fresh medium. Cells were selected in Neomycin for two weeks with fresh media being added 3-4 weeks and cells split 1:3 when reaching 80-90% confluency. Then cells were plated into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of medium fresh lentivirus media generated using pLVX-NAB2-STAT6-FLAG-Tight-Puro with 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G) per well was added to replace the old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, cells were disassociated with Trypsin and plated at a low density in a 15 cm dish.  Single cells were cultured with 0.5 ug/ml of puromycin for the next 2-3 weeks until colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened after addition of 1ug/mL Doxycline by verified by Western Blot. ATAC-seq was done without doxycycline treatment and after 2 days of 1ug/mL doxycycline treatment.


title: siPC1possiMRTFA_2_S14


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, EGR1, biol rep2


title: Col_27_T0_rep1


title: Col_27_T0_rep2


title: Col_17_T8_rep2


title: siPC2_4_S12


title: Col_17_T8_rep1


title: U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, ATAC, biol rep1


title: Col_17_T0_rep2


title: U2OS, pLVX-NAB2-STAT6, control, ATAC, biol rep2

description: ATAC in U2OS pLVX-NAB2-STAT6 cells in control conditions


title: siPC2_2_S10


title: U2OS, pLVX-NAB2-STAT6, control, ATAC, biol rep1


title: siPC1_A2_S9


title: CHIP_HTR13(H3)_17C

data_processing:
The raw reads obtained from the sequencing facilities were analysed in house. We first assessed the quality of reads using FastQC
(www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 reference genome using Bowtie2 (Langmead et al., 2009). Potential optical duplicates were removed using Picard, as described earlier. The read counts mapped to each bp in each sample was normalised by the sample’s genome-wide mappable reads coverage per bp, and used in the subsequent statistical analyses. The nucleosome and ChIP profiles were binned to generate a “pileup” ChIP profiles for different groups of genes/promoters using in-house R and Perl scripts.
Supplementary_files_format_and_content: bigWig

source_name: HTR13:HTR13::GFP seedlings

growth_protocol: Seedlings were grown at 17c in long days for 12 days and collected after 15min, 1hr or 4hrs of shift 17c, 27c or 37c.

extract_protocol:
Preparation the ChIP experiment was performed as described by Gendrel et al. (2002) with minor modifications. Plant material was immediately cross-linked when collected using 1% formaldehyde for 15min under vacuum. Chromatin was extracted from 1 g of cross-linked materials. For  MNAse-seq and CHIP-seq of: HTA11::HTA11-Flag, HTA11::HTA11-FLAG dek3-2, HTA11::HTA11-FLAG 35S::DEK3-CFP double mutant lines and H3.3-GFP, the chromatin was resuspended in MNase digestion buffer (20mM Tris-HCl [pH8], 50mM NaCl, 1mM DTT, 0.5% NP-40, 1mM CaCl2, 0.5mM phenylmethylsulfonyl fluoride (PMSF) and 1X protease inhibitor cocktail [Roche]), and digested with 0.4U/ml of micrococcal nuclease (MNase, Sigma, N3755) for 15 min. Digestion was stopped with 5 mM EDTA. MNase digestion was performed to obtain a mono-nucleosome resolution as MNase preferentially digests nucleosome-free DNA and the linker regions, whereas sequences bound by nucleosomes are relatively protected from the digestion. For MNAseseq samples have been used for library preparation directly after digestion. For DEK3::DEK3-CFP and 35S::DEK3-CFP CHIP-seq, chromatin was fragmented by sonication using a Bioruptor (Diagenode) in lysis buffer (10 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA [pH 8], 0.1% deoxycholate, and 1X protease inhibitor cocktail). All ChIPs were performed in a buffer containing 1 20mM Tris-HCl (pH8), 150mM NaCl, 2mM EDTA, 1% triton X-100 and 1X protease inhibitor cocktail. ChIP were performed for HTA11::HTA11-Flag using FLAG M2 magnetic beads (Sigma, M8823) and for DEK3::DEK3-CFP, 35S::DEK3-CFP, H3.3-GFP using anti GFP antibody (Abcam, ab290) coupled to a 1/1 mix of protein-A and protein-G Dynabeads (life technologies, 10001D and 10003D). All samples have been subsequently washed 2 times with low salt buffer (20mM Tris buffer (pH=8), 150mM NaCl, 0.1%SDS, 1% Triton) twice with high salt buffer (20mM Tris buffer (pH=8), 500mM NaCl, 0.1%SDS, 1% Triton), once with LiCl buffer (10mM Tris buffer (pH=8), 250mM LiCl, 1%Sodium deoxycholate, 1% NP40) and twice with TE buffer (10mM Tris buffer (pH=8), 1mM EDTA). The elution was done for anti-Flag ChIP with 100ng/ul of 3XFLAG in TE buffer and for anti-GFP ChIP with elution buffer (1% SDS, 0.1M NaHCO3). DNA was extracted using AMPure beads using a ratio of 2.3X as described previously.
MNAseseq and CHIPseq libraries have been prepared in house using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®  (#E7645). The libraries were sequenced using paired-end 75bp on NextSeq500 on site. CHIP 35S::DEK3-CFP, CHIP HTR5::HTR5-GFP and HTR13::HTR13-GFP libraries have been prepared using the TruSeq ChIP library preparation kit (IP-202-1012). CHIP HTR5::HTR5-GFP and HTR13::HTR13-GFP libraries were sequenced on a NextSeq 500 using PE 75bp. CHIP 35S::DEK3-CFP libraries were sequenced using on a NextSeq 500 SE 75bp.

tag: time of day

tag: protocol

value: sonication

value: Anti-GFP (Abcam, ab290)


title: CHIP_HTR5(H3.3)_27C_1hr_shift

source_name: HTR5:HTR5::GFP seedlings


title: RNA-seq_SP230-2_ITD-15_FLT3i

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Paired-end reads from RNA sequencing experiments were processed using Trimmomatic.
Processed reads were then aligned to the human genome (version hg38) using Hisat2 v2.2.1 (Kim et al. 2019; PMID:31375807) with default parameters.
Read counts were calculated using featureCounts with the options -s 2 -p and using gene models from ensembl as the reference transcriptome.
Assembly: hg38
Supplementary files format and content: Tab-Delimited files with gene IDs and read counts

source_name: CD34+ primary AML cells

growth_protocol: Cells were cukltered at 0.3-0.5 x 106 cells/ml on hMSC feeders in alpha-MEM (Lonza) supplemented with 12.5 % fetal calf serum, 12.5 % horse serum, 100 U/ml penicillin/streptomycin, 2 mM L-Glutamine (all Gibco), 1 μM hydrocortisone (Merck) and 57.2 μM β-mercaptoethanol (Merck), 20 ng/ml IL-3, G-CSF and TPO (Pepro Tech). Cells were cultured on hMSC feeders for 7 days prior to experiments. MV4-11 (DMSZ, AC102) and MOLM14 (DSMZ, ACC 777) were cultured in RPMI 1640 supplemented with 10% fetal calf serum, 2mM L-glutamine and 100 u/ml senicillin/streptomycin (all Gibco) at 37 ˚C with 5% CO2. Human embryonic kidney 293T (HEK293T) cells were cultured in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 0.11 mg ml–1 sodium pyruvate.

extract_protocol:
RNA extraction was done using a RNeasy Micro Plus kit (QIAGEN) where less than 50,000 cells were harvested, and a RNeasy Micro Plus kit (QIAGEN) for larger cell numbers.
RNA was quantified by nanodrop and QC’d using an Agilent RNA 6000 Pico Kit (Agilent, bioanalyser). Libraries for next generation sequencing were prepared using the NEBnext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) with the NEBNext® rRNA Depletion Kit v2 for low RNA input (<100 ng RNA), or the Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina) for higher RNA input. Libraries were quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to paired end sequencing on a Next Seq 2000 (PE 75) with a NextSeq High 150 v2.5 kit.

value: CD34+ primary AML cells


title: CHIP_HTR5(H3.3)_17C


title: CHIP_DEK3-OX17_CFP_27C_1hr_shift

source_name: 35S::DEK3-CFP(17) seedlings


title: siPC1_4_S8


title: CHIP_HTR13(H3)_27C_1hr_shift


title: siPC1possiMRTFA_1_S13


title: RNA-seq_SP230-1_ITD-15

value: Untreated


title: RNA-seq_ER232-2_ITD-16_FLT3i


title: CHIP_DEK3-OX9_CFP_27C_1hr_shift

source_name: 35S::DEK3-CFP(9) seedlings


title: CHIP_DEK3-OX17_CFP_17C


title: siPC1_2_S6


title: CHIP_DEK3-OX9_CFP_17C


title: siPC1_3_S7


title: CHIP_DEK3_CFP_27C_T8

source_name: DEK3::DEK3-CFP seedlings


title: RNA-seq_ER232-1_ITD-16


title: siPC2_3_S11


title: CHIP_DEK3_CFP_27C_T0


title: CHIP_DEK3_CFP_17C_T8


title: siPC1_1_S5


title: Col_17_T0_rep1


title: CHIP_DEK3_CFP_17C_T0


title: RNA-seq_D929-4_MV411_FLT3i_Rep2


title: Input_DEK3_CFP_27C_T8


title: Input_DEK3_CFP_17C_T8


title: NR_3_S3

value: Control


title: NR_4_S4


title: RNA-seq_D929-2_MV411_Untreated_Rep2


title: INPUT_HTA11-Flag_DEK3-OX17_27C_ZT0_rep2

value: MNase (mononucleosome)


title: Input_DEK3_CFP_17C_T0


title: Input_DEK3_CFP_27C_T0


title: RNA-seq_D929-1_MV411_Untreated_Rep1


title: INPUT_HTA11-Flag_DEK3-OX17_17C_ZT0_rep2


title: NR_2_S2

value: kidney


title: INPUT_HTA11-Flag_DEK3-OX17_27C_ZT0_rep1


title: NR_1_S1

value: Epithelial cell


title: INPUT_HTA11-Flag_dek3_27C_ZT0_rep2

source_name: dek3-2 HTA11::HTA11:FLAG seedlings


title: INPUT_HTA11-Flag_DEK3-OX17_17C_ZT0_rep1


title: RNA-seq_D770-9_ITD-17


title: Replicate 3

city: Shenzhen

first: PENG

last: DONG

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Shenzhen Institute of Advanced Technology

description: Smart-SCRB

library_source: transcriptomic single cell

data_processing:
Four plates were pooled together on a NextSeq 550 high-output flow cell or NextSeq 2000 P2-100 flow cell with 26 bp in read 1 and 50 bp in read 2. PhiX control library (Illumina) was spiked in at a final concentration of 7.5% to improve color balance in Read 1. Read 1 contains the spacer, barcode, and UMI and read 2 represents a cDNA fragment from the 3' end of the transcript. The entire experimental procedure was replicated two more times and ~400 cells were analyzed for each condition (control vs. auxin-treated).
Assembly: mm10
Supplementary files format and content: Tab-separated value and text files

organism: Mus musculus

growth_protocol: JM8.N4 mouse embryonic stem cells (mESCs) from the C57BL/6N strain and their genome-edited derivatives were routinely cultured in 60mm plates coated with 0.1% gelatin without feeders at 37°C and 5% CO2. The mESC culture medium was composed of the optimized knockout DMEM for mESCs, 15% ESC-qualified Fetal Bovine Serum, 1000 units of Leukemia inhibitory factor (LIF) , 1mM GlutaMAX , 0.1mM MEM nonessential amino acids , 0.1mM β-mercaptoethanol and Antibiotic-Antimycotic . 2i inhibitors were also added into the medium at final concentrations of 1uM for PD0325901 and 3uM for CHIR99021, respectively.

extract_protocol:
1ul harsh lysis buffer (50mM Tris (pH=8.0), 5mM EDTA (pH=8.0), 10mM DTT, 1% Tween-20, 1% Triton X-100, 0.1g/l proteinase K, 2.5mM dNTPs, and ERCC Mix (107-fold dilution) and 1ul 10mM barcoded RT primer was added to each well. Plates were incubated at 50°C for 5 mins to lyse cells and proteinase K was heat-inactivated by subsequently incubating at 80°C for 20 mins. To minimize contamination across wells, heavy-duty plate seals and qPCR compression pads (Thermo Fisher Scientific, Cat. 4312639) were used to seal the plates. The lysis reaction was mixed with 2ul reverse transcription master mix 5×buffer (Thermo Fisher Scientific, Cat. 11756500), 2ul 5M Betaine (Sigma-Aldrich, Cat. B0300-1VL), 0.2ul 50mM E5V6NEXT template switch oligo (Integrated DNA Technologies), 0.1ul 200U/ul Maxima H-RT (Thermo Fisher Scientific, Cat. EP0751), 0.1ul 40U/ul NxGen RNase Inhibitor, and 0.6ul nuclease-free water (Thermo Fisher Scientific, Cat. AM9932). The reaction system was then incubated at 42°C for 1.5 hrs, followed by 10 mins at 75°C to inactivate reverse transcriptase. PCR was performed by adding 10ul 2×HiFi PCR mix (Kapa Biosystems, Cat. 7958927001) and 0.5ul 60mM SINGV6 primer and running the following program: 98°C for 3 mins, 20 cycles of 98°C for 20 s, 64°C for 15 s, 72°C for 4 mins, with a final extension step off 5 mins at 72°C.
Single-cell cDNA was pooled by plate to make library. 600 pg cDNA from each sample plate was used in a modified Nextera XT (Illumina, Cat. FC-131-1024) library preparation but using the P5NEXTPT5 primer and the tagmentation time of 5 mins. The resulting libraries were purified following the Nextera XT protocol (0.6× ratio) and quantified by qPCR using Kapa Library Quantification kit (Kapa Biosystems, Cat. KK4824).

treatment_protocol: The plant auxin analog Indole-3-acetic acid (IAA) sodium salt was dissolved in ddH2O with a stock concentration of 500mM, aliquoted and stored at −20°C. To completely deplete endogeneous RAD21, cells were treated with IAA at a concentration of 500µM for 6 hrs.

tag: strain

value: mESC

value: Control and auxin-treated


title: INPUT_HTA11-Flag_dek3_27C_ZT0_rep1


title: INPUT_HTA11-Flag_dek3_17C_ZT0_rep2


title: RNA-seq_D1091-9_ITD-18_FLT3i_Rep2


title: INPUT_HTA11-Flag_dek3_17C_ZT0_rep1


title: Replicate 1

description: Smart-SCRB


title: RNA-seq_D1091-8_ITD-18_IL3_Rep2


title: INPUT_HTA11-Flag_27C_ZT0_rep1

source_name: Col0 HTA11::HTA11:FLAG seedlings


title: ChIP_Th1_D3_input_F_KO2

first: Vijay

last: Nagarajan

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

data_processing:
DNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
alignment: Sequencing data from ChIP-Seq were mapped onto mouse genome build mm10 using Bowtie 0.12.8 (reference #46). BigWig tracks were generated by the Hypergeometric Optimization of Motif EnRichment program (HOMER) (Reference #45) and visualized by IGV (Nature Biotechnology 29, 24–26 (2011)).
peaks: MACS (version 1.4.2) (Genome Biology volume 9, Article number: R137 (2008)) was used for peak calling of transcription factor ChIP-Seq using a P-value threshold of 1 x 10-5. Downstream analyses and graph generation were performed with HOMER and R.
Assembly: mm10
Supplementary files format and content: bigwig files for ChIP-seq

source_name: Th1 cells

extract_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10  ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
ChIP was performed for transcription factors CTCF (Millipore Sigma, #07-729), Rad21 (Abcam, #ab992) and p300 (Abcam, #ab14984) using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, #9005S). ChIP was performed for histone marks H3K27ac (Abcam, #ab4729), H3K27me3 (Thermo Fisher Scientific, #MA511198) and H3K4me1 (Abcam, #ab8895) using iDeal ChIP-seq Kit for Histones (Diagenode, #C01010051).
The purified enriched DNA was used to generate libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645) and NEBNext Multiplex Oligos for Illumina (NEB, #E6609).

treatment_protocol:
Toxoplasma gondii infection protocol: Wild type and IfngCTCFdel mice were inoculated with an average of 15 cysts of type II avirulent T. gondii strain ME-49 by intraperitoneal injection
LCMV infection protocol: LCMV (strain Armstrong) was thawed at 37°C and then injected into mice by intraperitoneal injection at the concentration 2 x 10^5 plaque-forming units (PFU) per mouse.

value: Spleen

value: Th1 cells

tag: culture condition

value: ex vivo

tag: chip antibody vendor

tag: chip antibody cat.#


title: Replicate 2

description: Smart-SCRB

tag: cell line

tag: cell type


title: RNA-seq_D929-3_MV411_FLT3i_Rep1

tag: genotype


title: INPUT_HTA11-Flag_17C_ZT0_rep2


title: RNA-seq_D1091-7_ITD-18_Untreated_Rep2

tag: treatment


title: INPUT_HTA11-Flag_17C_ZT0_rep1


title: ChIP_Th1_D3_input_F_KO1


title: CHIP_HTA11-Flag_DEK3-OX17_27C_ZT0_rep2

value: Anti-FLAG M2 Magnetic Beads (M8823 SIGMA)


title: RNA-seq_D1091-6_ITD-18_RASi_IL3_Rep1

value: RASi + IL3


title: RNA-seq_D787_ITD-17_FLT3i


title: CHIP_HTA11-Flag_DEK3-OX17_17C_ZT0_rep2


title: ChIP_Th1_D3_input_F_WT2


title: CHIP_HTA11-Flag_DEK3-OX17_17C_ZT0_rep1


title: RNA-seq_D1091-4_ITD-18_FLT3i_IL3_Rep1

value: FLT3i + IL3


title: ChIP_Th1_D3_input_F_WT1


title: CHIP_HTA11-Flag_dek3_27C_ZT0_rep2

value: T0 (just before lights turn on)


title: RNA-seq_D1091-5_ITD-18_RASi_Rep1

value: RASi


title: CHIP_HTA11-Flag_dek3_27C_ZT0_rep1


title: INPUT_HTA11-Flag_27C_ZT0_rep2


title: CHIP_HTA11-Flag_dek3_17C_ZT0_rep1


title: CHIP_HTA11-Flag_dek3_17C_ZT0_rep2


title: RNA-seq_D1091-3_ITD-18_FLT3i_Rep1


title: ChIP_Th1_D3_H3K4me3_F_KO2

value: Millipore Sigma


title: ChIP_Th1_D3_H3K4me3_F_KO1


title: CHIP_HTA11-Flag_27C_ZT0_rep2


title: CHIP_HTA11-Flag_27C_ZT0_rep1


title: RNA-seq_D1091-2_ITD-18_IL3_Rep1

value: CD34+ primary AML cells


title: CHIP_HTA11-Flag_17C_ZT0_rep2


title: High 2

city: Chengdu

first: Yang

last: Li

address: No.37 Guoxue Alley, Wuhou District,

institute: West China Hospital of Sichuan University

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic location
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: Rattus_norvegicus Ensembl relaese-94
Supplementary files format and content: Excel file reports sequence and normalized expression of all miRNAs

organism: Rattus norvegicus

source_name: Blood

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq2000/2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: 18 10-12-weeks old SD rats were randomly divided into six groups. The normal control group (rats were not subjected to any disposal, Normal group); the blank control group (rats were administered intragastrically by of propylthiouracil PTU  0.01/kg one day for 28 days, Blank group); the positive drug control group (rats subjected to nodular goiter were administered intragastrically with levothyroxin sodium tablets (LST) 0.07 mg/kg one day for one day 28 days, LST group); the light concentration of QMTG prescription group (rats subjected to goiter were administered intragastrically with QMTG 0.63 g/kg one day for 28 days, Light group); the moderate concentration of QMTG prescription group (rats subjected to nodular goiter were administered with intragastrically QMTG 1.26 g/kg  one day for 28 days, Moderate group); the high concentration of QMTG prescription group (rats subjected to nodular goiter were administered intragastrically with QMTG 2.52 g/kg  one day for 28 days, High group).

value: Sprague-Dawley

value: Blood

value: High SHB

tag: disease state

value: PTU-induced model


title: RNA-seq_D1091-1_ITD-18_Untreated_Rep1

value: Untreated


title: High 3

tag: tissue


title: CHIP_HTA11-Flag_17C_ZT0_rep1

value: MNase (mononucleosome)


title: CHIP_HTA11-Flag_DEK3-OX17_27C_ZT0_rep1


title: RNA-seq_D1091-12_ITD-18_RASi_IL3_Rep2


title: ChIP_Th1_D3_H3K4me3_F_WT1


title: RNA-seq_D1091-11_ITD-18_RASi_Rep2


title: Moderate 2

value: Moderate SHB


title: Moderate 1


title: ChIP_Th1_D3_H3K27me3_F_KO1

value: Spleen

value: Thermo Fisher Scientific


title: ChIP_Th1_D3_H3K27me3_F_KO2

value: Th1 cells

value: ex vivo


title: RNA-seq_D1091-10_ITD-18_FLT3i_IL3_Rep2


title: Moderate 3


title: High 1


title: Light 3

treatment_protocol: 18 10-12-weeks old SD rats were randomly divided into six groups. The normal control group (rats were not subjected to any disposal, Normal group); the blank control group (rats were administered intragastrically by of propylthiouracil PTU  0.01/kg one day for 28 days, Blank group); the positive drug control group (rats subjected to nodular goiter were administered intragastrically with levothyroxin sodium tablets (LST) 0.07 mg/kg one day for one day 28 days, LST group); the light concentration of QMTG prescription group (rats subjected to goiter were administered intragastrically with QMTG 0.63 g/kg one day for 28 days, Light group); the moderate concentration of QMTG prescription group (rats subjected to nodular goiter were administered with intragastrically QMTG 1.26 g/kg  one day for 28 days, Moderate group); the high concentration of QMTGprescription group (rats subjected to nodular goiter were administered intragastrically with QMTG 2.52 g/kg  one day for 28 days, High group).

value: Light SHB


title: Light 1


title: ChIP_Th1_D3_H3K27me3_F_WT1


title: RNA-seq_D1063-9_MOLM14_RASi_Rep1


title: ChIP_Th1_D3_H3K4me3_F_WT2


title: LST 3

value: LST


title: LST 1


title: Blank 3

value: PTU


title: Light 2


title: RNA-seq_D1063-8_MOLM14_FLT3i_IL3_Rep2

value: FLT3i + IL3


title: ChIP_Th1_D3_H3K4me1_F_KO1

value: Abcam


title: Blank 2


title: LST 2


title: ChIP_Th1_D3_H3K4me1_F_KO2


title: ChIP_Th1_D3_H3K27me3_F_WT2


title: Normal 3

value: normal control

value: no PTU-induced model


title: RNA-seq_D1063-7_MOLM14_FLT3i_IL3_Rep1


title: ChIP_Th1_D3_H3K4me1_F_WT2


title: RNA-seq_D1063-6_MOLM14_FLT3i_Rep2


title: Blank 1

value: Sprague-Dawley

value: Blood


title: Normal 2


title: Normal 1


title: ChIP_Th1_D3_H3K4me1_F_WT1


title: RNA-seq_D1063-4_MOLM14_IL3_Rep2


title: ChIP_Th1_D3_H3K27ac_F_KO2

data_processing:
DNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
alignment: Sequencing data from ChIP-Seq were mapped onto mouse genome build mm10 using Bowtie 0.12.8 (reference #46). BigWig tracks were generated by the Hypergeometric Optimization of Motif EnRichment program (HOMER) (Reference #45) and visualized by IGV (Nature Biotechnology 29, 24–26 (2011)).
peaks: MACS (version 1.4.2) (Genome Biology volume 9, Article number: R137 (2008)) was used for peak calling of transcription factor ChIP-Seq using a P-value threshold of 1 x 10-5. Downstream analyses and graph generation were performed with HOMER and R.
Assembly: mm9
Supplementary files format and content: bigwig files for ChIP-seq


title: U251 shNUDT21 3

city: Houston

first: Venkata

middle: Soumith

last: Jonnakuti

state: TX

address: 2255 Braeswood Park Drive

institute: Baylor College of Medicine

description: treatment U251 cells with NUDT21 siRNA; sample 3

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
Samtools were used to sort, convert and index alignment files
Assembly: GRCh38

source_name: Fibroblast-like morphology

growth_protocol: U251 and LN229 were grown in DMEM+10%FBS.  Low passage numbers were attained and cells were not grown for more than 2 months until a new passage was thawed out.

extract_protocol:
72hrs after RNAi, cells were harvested for either Western Blot using SDS loading buffer or for RNA isolation using TriZol.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: Cells were transfected with either control siRNA or siRNA targeting NUDT21 using Lipofectamine 2000.

tag: culture duration

value: 60 days

tag: shRNA


title: U251 shNUDT21 2

description: treatment U251 cells with NUDT21 siRNA; sample 2


title: RNA-seq_D1063-3_MOLM14_IL3_Rep1


title: ChIP_Th1_D3_H3K27ac_F_KO1

tag: chip antibody


title: RNA-seq_D1063-2_MOLM14_Untreated_Rep2

value: Untreated


title: U251 Scramble 2

description: control U251 cells with scramble siRNA; sample 2

value: Scramble


title: U251 Scramble 3

description: control U251 cells with scramble siRNA; sample 3


title: ChIP_Th1_D3_H3K27ac_F_WT2


title: U251 Scramble 1

description: control U251 cells with scramble siRNA; sample 1


title: U251 shNUDT21 1

description: treatment U251 cells with NUDT21 siRNA; sample 1


title: RNA-seq_D1063-1_MOLM14_Untreated_Rep1


title: ChIP_Th1_D3_H3K27ac_F_WT1


title: LN229 shNUDT21 2

description: treatment LN229 cells with NUDT21 siRNA; sample 2

source_name: Epithelial morphology


title: RNA-seq_D1063-12_MOLM14_RASi_IL3_Rep2

value: RASi + IL3


title: RNA-seq_D1063-5_MOLM14_FLT3i_Rep1


title: RNA-seq_D1063-11_MOLM14_RASi_IL3_Rep1


title: LN229 shNUDT21 3

description: treatment LN229 cells with NUDT21 siRNA; sample 3


title: LN229 Scramble 3

description: control LN229 cells with scramble siRNA; sample 3


title: LN229 Scramble 1

description: control LN229 cells with scramble siRNA; sample 1


title: RNA-seq_D1063-10_MOLM14_RASi_Rep2

value: RASi


title: LN229 Scramble 2

description: control LN229 cells with scramble siRNA; sample 2


title: Den_14d 2

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: skeletal muscle

extract_protocol:
RNA was harvested using TRIzol reagent (Sigma, T9424). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skeletal muscle

value: Muscle denervation (14 d)

value: WT mice


title: Den_14d 3


title: ChIP_360_Input_WT_Th1_rep2

value: Spleen

value: Th1 cells

value: ex vivo


title: ITD-17_FLT3i

data_processing:
Single-end reads were processed for quality control using Trimmomatic and aligned to the human genome (version hg38) using bowtie2 with the option --very-sensitive-local.
PCR duplicates were removed from alignments using the MarkDuplicates function in Picard.
Peaks were identified using MACS2 with the parameters --nomodel -B --tracklist.
Assembly: hg38
Supplementary files format and content: BedGraph files of read pileups from MACS2
Library strategy: DNaseI-seq

source_name: CD34+ AML primary cells

growth_protocol: Cells were cukltered at 0.3-0.5 x 106 cells/ml on hMSC feeders in alpha-MEM (Lonza) supplemented with 12.5 % fetal calf serum, 12.5 % horse serum, 100 U/ml penicillin/streptomycin, 2 mM L-Glutamine (all Gibco), 1 μM hydrocortisone (Merck) and 57.2 μM β-mercaptoethanol (Merck), 20 ng/ml IL-3, G-CSF and TPO (Pepro Tech). Cells were cultured on hMSC feeders for 7 days prior to experiments

extract_protocol:
DNaseI-seq was performed on purified CD34+ or CD117+ blasts from fresh patient samples. Live cells were added directly to a solution of DNase I in dilute NP40, digested for 3 min at 22˚C, and the reactions then terminated by addition of SDS to 0.5%. DNase I (Worthington Biochemical Corporation) was typically used in the range of 2-6 μg/ml using a final 1.5 x 107 cells/ml. Cell lysates were treated with RNAse A for 1 h at 37 ˚C and DNA was isolated by phenol/chloroform extraction.
DNaseI-Seq samples were generated from a size selection of DNase I-digested DNA fragments comprised within a range of 100 to 250 bp (not including linkers) and libraries were made using a Kapa Hyper prep kit (Roche) according to manufacturers instructions. 12-14 cycles of PCR amplification were used and 200-450 bp fragments were size selected by gel electrophoresis o na 1.5% agarose gel. Libraries were validated by qPCR and quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to sequencing on a Nextseq 2000 75 using a NextSeq 500/550 High output kit.

value: CD34+ AML primary cells


title: ChIP_361_Input_CTCFdel_Th1_rep1


title: WT Innervated 2

value: Innervated control muscles


title: Den_14d 1


title: ChIP_359_Input_WT_Th1_rep1


title: WT Innervated 1


title: NRF1-PAX4 double KD, denervated 3

value: Dmut

value: Muscle denervation (10 d)

value: NRF1PAL-PAX4 double KD mice


title: ChIP_358_Rad21_CTCFdel_Th1_rep2

value: Abcam


title: D760_ITD-17


title: D631_ITD-16_FLT3i


title: NRF1-PAX4 double KD, denervated 1


title: NRF1 KD denervated 3

value: NRFkd

value: NRF1PAL KD mice


title: ChIP_356_Rad21_WT_Th1_rep2


title: ChIP_362_Input_CTCFdel_Th1_rep2


title: LN229 shNUDT21 1

description: treatment LN229 cells with NUDT21 siRNA; sample 1

value: 60 days


title: ChIP_357_Rad21_CTCFdel_Th1_rep1


title: NRF1-PAX4 double KD, denervated 2


title: D552_ITD-15

value: Untreated


title: NRF1 KD denervated 1


title: ChIP_355_Rad21_WT_Th1_rep1


title: WT con denervated 3

value: con


title: P1482_MOLM14_RUNX1_ChIP_Untreated

data_processing:
Raw sequencing reads were trimmed to remove low quality sequences and adaptors using Trimmomatic v0.39 (Bolger et al. 014; PMID:24695404).
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.5 (Langmead et al. 2012; PMID:22388286) with the parameter --very-sensitive-local.
Potential PCR duplicates were identified and removed from alignments using the MarkDuplicates function in Picard tools v2.26.10 (https://broadinstitute.github.io/picard).
Peak calling was performed using MACS v2.2.7.1 (Zhang et al. 2008; PMID:18798982) using the option -B --trackline -q 0.01.
Assembly: hg38
Supplementary files format and content: BedGraph files of read pileups from MACS2

growth_protocol: MV4-11 (DMSZ, AC102) and MOLM14 (DSMZ, ACC 777) were cultured in RPMI 1640 supplemented with 10% fetal calf serum, 2mM L-glutamine and 100 u/ml senicillin/streptomycin (all Gibco) at 37 ˚C with 5% CO2. Human embryonic kidney 293T (HEK293T) cells were cultured in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 0.11 mg ml–1 sodium pyruvate.

extract_protocol:
Cells were treated with 10 nM gilteritinib or doxycycline to induce RASiDAb in the presence or absence of 10 ng/ml IL-3 for 24 h prior after which 20 million cells were harvested and crosslinked in 1% formaldehyde solution (methanol-free from Pierce, Thermo Scientific). 400 mM of glycine (Merck) was added, and cells were washed twice with PBS (Merck) after which pellets were frozen at -80 °C. Crosslinked cells were resuspended at 1x107 cells/ml in Buffer A (10 mM HEPES, 10 mM EDTA, 0.5 mM MEGTA, 0.25 % Triton- 100, 1x complete mini protease inhibitor cocktail (PIC) (Merck) pH 8.0) and incubated at 4 °C for 10 minutes prior to centrifugation at 500 xG for 10 min. This step was repeated with Buffer B (10 mM HEPES, 200 mM NaCl, 1 mM EDTA, 0.5 mM MEGTA, 0.01 % Triton-X 100, 1x PIC, pH 8.0) and after centrifugation 2 x 106 cells were resuspended in 300 μl IP buffer I (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 0.25 % SDS, 1x PIC, pH 8.0) and sonicated using a Diagenode Bioruptor Pico sonicator for 4 cycles (30 sec on 30 sec off) before centrifugation for 10 min at 16,000 xG. The supernatant was then collected and 600 μl IP Buffer II (25 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1 % Triton-X 100, 7.5 % Glycerol, 1x PIC, pH 8.0) was added prior to immunoprecipitation. For immunoprecipitations 15 μl of Dynabeads-Protein G were washed twice with 500 μl 50 mM citrate phosphate buffer pH 5 and resupended in 15 μl citrate phosphate buffer with 4 μg anti-RUNX1 antibody (ab23980, Abcam) or (Invitrogen, MA5-15055) and 0.5% acetyl-BSA before incubation at 4 °C for 2 h. After incubation, dynabeads were washed with 500 μl pH 5 citrate phosphate buffer and resuspended in 15 μl citrate phosphate buffer with 0.5 % BSA before 555 μl of sonicated chromatin was added and incubated at 4 °C for ~ 16 h. After the incubation the dynabeads are washed sequentially with 500 μl of: Wash buffer 1 (20 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 1% Triton-X 100, 0.1% SDS, pH 8.0) once, Wash buffer 2 (20 mM Tris-HCl, 500 mM NaCl, 20 mM EDTA, 1 % Triton-X 100, 0.1 % SDS, pH 8) twice, LiCl buffer (10 mM Tris-HCl,250 mM LiCl, 1 mM EDTA, 0.5 % NP-40, 0.5 % Na-deoxycholate, pH 8.0) once, TE/NaCl wash buffer (10 mM Tris-HCl, 50 mM NaCl, 1 mM EDTA, pH 8.0) twice. After these washes DNA was eluted from the dynabeads using 100 μl elution buffer (100 mM NaHCO3, 1% SDS). 200 mM NaCl and 500 μg/ml proteinase K were added to the eluant and the sample was reverse crosslinked at 65 °C for >4h. DNA was then purified by ampure (1.8x).
Libraries for next generation sequencing were prepared using a Kapa Hyper prep kit (Roche) according to manufacturers instructions. 16 cycles of PCR amplification were used and 200-450 bp fragments were size selected by gel electrophoresis. Libraries were validated by qPCR and quantified using the High Sensitivity DNA kit (Agilent) and Kapa Library Quantification kit (Roche) prior to sequencing on a Nextseq 2000 75 using a NextSeq 500/550 High output kit.

tag: target

tag: antibody

value: Abcam, ab23980


title: WT con denervated 2

value: skeletal muscle


title: WT con denervated 1

value: WT mice


title: ChIP_354_p300_CTCFdel_Th1_rep2

value: Spleen


title: PAX4 KO denervated 3

value: PAX4 KO mice


title: P1482_MOLM14_RUNX1_ChIP_RAS_iDAB

value: RAS iDAB


title: ChIP_353_p300_CTCFdel_Th1_rep1

value: Th1 cells

value: ex vivo


title: PAX4 KO denervated 2


title: PAX4 KO denervated 1


title: WT denervated 3


title: ChIP_352_p300_WT_Th1_rep2


title: D578_ITD-15_FLT3i

value: CD34+ AML primary cells


title: P1482_MOLM14_RUNX1_ChIP_FLT3i


title: ChIP_351_p300_WT_Th1_rep1


title: P1482_MOLM14_RUNX1_ChIP_EmptyVector

value: Empty Vector


title: WT denervated 1

value: Muscle denervation (10 d)


title: NRF1 KD denervated 2


title: WT Con Innervated 1

value: Innervated control muscles


title: ChIP_350_CTCF_CTCFdel_Th1_rep2

value: anti-CTCF

value: Millipore Sigma


title: P1383_MV411_cFOS_ChIP_Untreated_Rep2

value: cFOS

value: Invitrogen, MA5-15055


title: P1383_MV411_cFOS_ChIP_FLT3i_Rep2


title: WT Con Innervated 2


title: ChIP_349_CTCF_CTCFdel_Th1_rep1


title: RNA-Seq of mus musculus:  Peritoneal macrophages with NC

city: Shanghai

first: Qihang

last: Zhao

address: 800 xiangyin road

institute: National laboratory of medical immunology

description: RNA-Seq of totol cell fraction of WT mouseperitoneal macrophages.

data_processing:
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS)
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: mouse peritoneal macrophages

extract_protocol:
RNA was harvested using TriZOL. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared according ro BGI company's standard protocols.

value: mouse peritoneal macrophages

value: macrophages

value: C57 B6/L WT

value: NC


title: RNA-Seq of mus musculus: Peritoneal macrophages with sitmulation of SeV

description: RNA-Seq of totol cell fraction of WT mouseperitoneal macrophages treat with Sev.

value: SEV(MOI=1) for 12h


title: ChIP_348_CTCF_WT_Th1_rep2

value: Spleen


title: Tes_UP7

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

description: mRNA sequencing

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNAseq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulat
Assembly: mice
Supplementary files format and content: excel sheet of read counts

source_name: mRNA from testis of hindlimb unloaded mice treated with 4-phenyl butyrate

growth_protocol: 4-month-old, male c57BL/6j mice into ground-based controls (n = 3) and Hind limb uploaded (HU) mice. HU mice were further divided into two groups and treated with either PBS as the vehicle (HU-v; n = 3) or 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections) (n = 3).

extract_protocol:
Total mRNAs were extracted from testis of the three groups of mice
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directiona

treatment_protocol: HU (n=3) mice were injected with 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections)

value: Testis

tag: agent

value: 4-phenyl butyrate


title: P1137_MV411_cFOS_ChIP_Untreated_Rep1

value: Untreated


title: ChIP_347_CTCF_WT_Th1_rep1

value: Th1 cells

value: ex vivo


title: Tes_UP6

description: mRNA sequencing


title: P1482_MOLM14_RUNX1_ChIP_FLT3i_IL3

value: Abcam, ab23980

value: FLT3i + IL3


title: P1137_MV411_cFOS_ChIP_FLT3i_Rep1


title: Tes_U24

description: mRNA sequencing

source_name: mRNA from tetis of hindlimb unloaded mice treated with PBS as vehicle

value: PBS


title: Th2_D10_K27Ac_141104_0303_s30

source_name: Th2 cells

value: Th2 cells

value: Abcam


title: WT denervated 2

value: skeletal muscle

value: Muscle denervation (10 d)

value: WT mice


title: Tes_U14

description: mRNA sequencing


title: D929-4_MV411_FLT3i_Rep2

data_processing:
Single-end reads from ATAC-Seq experiments were trimmed with Trimmomatic and aligned to the human genome (version hg38) using Bowtie2 with the --very-sensitrive-local parameter.
Potential PCR duplicates were identified and removed from alignments using the MarkDuplicates function in Picard.
Peak calling was then carried out using MACS2 with the options --nomodel --shift -100 --extsize 200 -B --trackline.
Assembly: hg38
Supplementary files format and content: BedGraph files of read pileups from MACS2

extract_protocol:
Cells were treated with inhibitors in the presence or absence of IL-3 for 24 h prior to harvest. Omni ATAC-seq was performed as in Corces et al. Briefly, cells were washed in ATAC resuspension buffer (RSB) (10mM Tris-HCl pH7.5, 10mM NaCl and 3mM MgCl2) and then lysed for 3 minutes on ice in RSB buffer with 0.1% NP-40, 0.1% Tween-20. Then the cells were washed with 1ml of ATAC wash buffer consisting of RSB with 0.1% Tween-20. Then the nuclear pellet was resuspended in ATAC transposition buffer consisting of 25μl TD buffer and a concentration of Tn5 transposase enzyme (Illumina) related to the number of input cells, 16.5 μl PBS, 5 μl water, 0.1% tween-20 and 0.01% digitonin and then incubated on a thermomixer at 37°C for 30 minutes. The transposed DNA was then amplified by PCR amplification up to ¼ of maximum amplification, as assessed by a qPCR side reaction.
The library was purified using a QIAquick PCR cleanup kit (QIAGEN) followed by ampure (Beckman Coulter) and analysed on a Next Seq 2000 75 using a NextSeq 500/550 High output kit.


title: Tes_U9

description: mRNA sequencing


title: WT Con Innervated 3

value: Innervated control muscles


title: Th2_D10_K27Ac_141007_0175_s19


title: Tes_C13

description: mRNA sequencing

source_name: mRNAs from testis of Ground-based control mice


title: Th2_D10_K27Ac_140108_0090_s4


title: D929-3_MV411_FLT3i_Rep1


title: D929-2_MV411_Untreated_Rep2


title: Tes_C7

description: mRNA sequencing


title: D929-1_MV411_Untreated_Rep1


title: Th2_D7_K27Ac_141007_0175_s31


title: D1091-9_ITD-18_FLT3i_Rep2

source_name: CD34+ primary AML cells

value: CD34+ primary AML cells


title: Th2_D7_K27Ac_141104_0303_s28


title: D1091-8_ITD-18_IL3_Rep2


title: Th2_D7_K27Ac_131213_0220_s4


title: Th2_D5_K27Ac_141007_0175_s27


title: Tes_UP5

description: mRNA sequencing


title: Th2_D5_K27Ac_141007_0175_s24


title: D1091-7_ITD-18_Untreated_Rep2


title: Th2_D5_K27Ac_140108_0090_s3


title: D1091-5_ITD-18_RASi_Rep1

value: RASi


title: D1091-3_ITD-18_FLT3i_Rep1


title: D1091-4_ITD-18_FLT3i_IL3_Rep1


title: Th2_D3_K27Ac_141007_0175_s15

value: Spleen


title: Th2_D3_K27Ac_131213_0220_s3


title: D1091-2_ITD-18_IL3_Rep1


title: Tes_C9

description: mRNA sequencing

value: Testis


title: D1091-12_ITD-18_RASi_IL3_Rep2

value: RASi + IL3


title: Th2_D1_K27Ac_140124_0092_s3


title: Th2_D1_K27Ac_141007_0175_s14


title: Th2_D1_K27Ac_141104_0303_s20


title: D1091-10_ITD-18_FLT3i_IL3_Rep2


title: D1091-11_ITD-18_RASi_Rep2


title: Th1_D10_K27Ac_141104_0303_s29


title: Th1_D10_K27Ac_141007_0175_s17


title: D1063-8_MOLM14_FLT3i_IL3_Rep2


title: Th1_D7_K27Ac_141104_0303_s27


title: D1063-7_MOLM14_FLT3i_IL3_Rep1


title: Th1_D7_K27Ac_141007_0175_s29


title: Th1_D7_K27Ac_131213_0220_s2


title: D1063-9_MOLM14_RASi_Rep1


title: D1063-5_MOLM14_FLT3i_Rep1


title: D1063-6_MOLM14_FLT3i_Rep2


title: D1091-6_ITD-18_RASi_IL3_Rep1


title: Th2_D3_K27Ac_141007_0175_s23


title: Th1_D5_K27Ac_141007_0175_s16


title: D1063-3_MOLM14_IL3_Rep1


title: D1063-4_MOLM14_IL3_Rep2


title: Th1_D5_K27Ac_141007_0175_s25


title: D1091-1_ITD-18_Untreated_Rep1

value: Untreated


title: D1063-2_MOLM14_Untreated_Rep2


title: Th1_D3_K27Ac_141104_0303_s21

value: Th1 cells


title: Th1_D3_K27Ac_141007_0175_s22

value: ex vivo


title: Th1_D5_K27Ac_140108_0090_s1


title: D1063-12_MOLM14_RASi_IL3_Rep2


title: Th1_D3_K27Ac_131213_0220_s1


title: D1063-10_MOLM14_RASi_Rep2


title: Th1_D1_K27Ac_140124_0092_s1


title: Th1_D1_K27Ac_141007_0175_s13


title: Th1_D10_K27Ac_140108_0090_s2


title: OS152, nuclei, m6dA methylated, rep8, 2.2 polymerase

first: Arjun

middle: S

last: Nanda

state: California

address: 1700 Owens St

department: Gladstone Institute for Data Science & Biotechnology

institute: Gladstone Institutes / UCSF

description: OS152 cell line from E Alejandro Sweet-Cordero Lab, UCSF.

data_processing:
Demultiplexing subreads BAM files with lima (v2.6.0)
Generating circular consensus sequences (CCS) using ccs (v6.4.0) with kinetic information
Extracting kinetic information from CCS reads using the SAMOSA-ChAAT computational pipeline
Aligning CCS reads to a modified version of the hg38 reference genome with the contaminant contig KI270752.1 removed using pbmm2 (v.1.9.0)
Assembly: hg38
Supplementary files format and content: *_full.pickle: Python pickle files containing IPD measurements for each base in the forward and reverse strands per CCS read
Supplementary files format and content: *_zmwinfo.pickle: Python pickle containing a  dataframe with length, # of  passes, and mean IPD per base per CCS read

source_name: F

growth_protocol: OS152 cells were cultured in standard 1x DMEM supplemented with 10% Fetal Bovine Serum and 1% 100x Penicillin-Streptomycin-Glutamine.

extract_protocol:
Tagmented nuclei were pre-treated with 10uL RNaseA at 37°C for 15 minutes, then purified with 2.5uL Proteinase K (20mg/mL), 2.5uL 10% SDS, and 2.5uL 0.5mM EDTA at 60°C for 1-2 hours with continuous shaking at 1000 rpm. DNA was extracted with 2x SPRI bead cleanup.
Tagmented fragments were gap-repaired using Phusion DNA polymerase and Taq Ligase, or T4 DNA polymerase and Ampligase, at 37ºC for 1hr, digested with Exonuclease III at 37ºC for 1hr, then cleaned up using Ampure PB. Library quality was assessed with Qubit 1x High Sensitivity DNA Assay and Agilent Bioanalyzer High Sensitivity DNA kit.

treatment_protocol:
Isolated OS152 nuclei were methylated (10uL EcoGII per 1-2e6 nuclei) with non-specific adenine methyltransferase EcoGII (New England Biolabs, HC stock 2.5e4U/mL) at 37°C for 30 minutes, supplemented with SAM to 1.16mM (NEB) after 15 minutes.
Isolated nuclei (methylated or unmethylated) were tagmented with H-Tn5-R27S,E54K,L372P (QB3 MarcoLab) at 55°C for 1hr.

value: F

value: OS152 cell line

value: metastatic osteosarcoma cell line

value: MYC amplified, CN40

value: m6dA methylated


title: OS152, nuclei, m6dA methylated, rep7, 2.2 polymerase


title: naïve_CD4_D0_K27Ac_140207_0096_s07

source_name: Naïve T cells

value: naive T cells

value: Abcam


title: OS152, nuclei, m6dA methylated, rep5, 2.2 polymerase


title: naïve_CD4_D0_K27Ac_141007_0175_s9


title: naïve_CD4_D0_K27Ac_140610_0127_s11


title: OS152, nuclei, m6dA methylated, rep4, 2.2 polymerase


title: OS152, nuclei, m6dA methylated, rep2, 2.2 polymerase


title: OS152, nuclei, m6dA methylated, rep1, 2.2 polymerase


title: 95T_Micro3,Rhesus Macauqe,12-days SIV infection,acute-infection

city: Omaha

first: Howard

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: Mmul10, NCBI RefSeq assembly and SIVmac251
Supplementary files format and content: FASTQ files contain the sequenced data
Supplementary files format and content: H5 files contain feature and cell barcode matrix

organism: Macaca mulatta

source_name: Brain

extract_protocol:
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the cryopreserved brains (104T, 111T) and fresh brains (92T, 93T, 94T, 95T). Isolates were immunomagnetically enriched for CD45+CD11b+ cells. The CD20 negative cells that were positive for either CD45 or CD11b or both CD45 and CD11b were collected for microglial/macrophages library preparations.
Post-sorting, isolates were concentrated to approximately 1000 cells per µL, and assessed by trypan blue for viability and concentration. Based on 10× Genomics parameters targeting 8000 cells, the ideal volume of cells was loaded onto the 10× Genomics (Pleasanton, CA, USA) Chromium GEM Chip and placed into the Chromium Controller for cell capturing and library preparation. This occurs through microfluidics and combining with Single Cell 3’ Gel Beads containing unique barcoded primers with a unique molecular identifier (UMI), followed by lysis of cells and barcoded reverse transcription of RNA, amplification of barcoded cDNA, fragmentation of cDNA to 200 bp, 5’ adapter attachment, and sample indexing as the manufacturer instructed with version 3 reagent kits. The prepared libraries were then sequenced using Illumina (San Diego, CA, USA) Nextseq550 and Novaseq6000 sequencers.

treatment_protocol: Three acute-infected rhesus macaques (93T, 94T, and 95T) were intravenously inoculated with SIVmac251

value: Brain

value: CD11b and/or CD45 positive cells

value: 12-days SIV infection


title: Fin Fold, IgG, Cut&Tag, 24HPF, REP3

city: Rochester, NY

first: Phu

middle: T

last: Duong

state: New York

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Raw fastq files were mapped using bowtie2 using danRer11 build outputting SAM files
SAM files were converted to sorted BAM files using SAMtools and then further filtered by Picard's MarkDuplicates
bigWig files were generated using deeptools' bamcoverage with the setting --normalizeUsing RPKM
Peaks were called using MACS2's bdgpeakcall
Picard-filtered BAM files were processed by deeptools' multibigwigsummary to create RPKM matrix for R's custom scripts to make visualizations
Assembly: danRer11
Supplementary files format and content: bigWig

organism: Danio rerio

source_name: caudal fin folds

growth_protocol: Adult Zebrafish were housed with a normal light/dark cycles and ad libitum access to food supply.

extract_protocol:
Cells were digested with Liberase DH and Collegnase IV aat 34oC for 1 hour and then filtered with 70um mesh. The cells were centrifugated, washed, and incubated in Nuclear extraction buffer.
Libraries were prepared for sequencing using standard CUT&TAG and Illumina protocols
CUT&Tag with IgG and H3K4me3

treatment_protocol: Adult caudal fins are amputated at 50%. Uninjured and 2 days post-amputation fins are collected. For embryo fin fold samples, caudal fin folds are amputated at 24  hours post-fertilization.

value: caudal fin folds

value: WT

value: 24h post amptuation


title: Caudal fin fold, 24hpf, rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and mapped to danRer11 using STAR-aligner
Sorted BAM files generated by STAR were processed by deeptools' multibigwigsummary to create RPKM matrix for R's custom scripts to make visualizations
bigWig files were also generated using deeptools' bamcoverage with the setting --normalizeUsing RPKM
Assembly: danRer11
Supplementary files format and content: bigWig

source_name: fin fold

extract_protocol:
Fin folds were homogenized immediately after dissection and RNA was extracted using Trizol reagent. .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: caudal fin folds were amputated with 24 hour post-fertilization embryos

value: fin fold


title: Caudal fin fold, 24hpf, rep1


title: D1063-1_MOLM14_Untreated_Rep1

value: Untreated


title: Fin Fold, IgG, Cut&Tag, 24HPF, REP2


title: Fin Fold, IgG, Cut&Tag, 24HPF, REP1


title: Th1_D1_K27Ac_141104_0303_s19

source_name: Th1 cells

value: Spleen

value: Th1 cells


title: 95T_Micro2,Rhesus Macauqe,12-days SIV infection,acute-infection


title: OS152, nuclei, m6dA methylated, rep6, 2.2 polymerase

value: F


title: Adult Fin, IgG, Cut&Tag, 2DPA, REP1

source_name: caudal fins

value: caudal fins

value: 2d post amputation


title: Adult Fin, IgG, Cut&Tag, 2DPA, REP3


title: 95T_Micro1,Rhesus Macauqe,12-days SIV infection,acute-infection


title: 94T_Micro2,Rhesus Macauqe,12-days SIV infection,acute-infection


title: Adult Fin, IgG, Cut&Tag, 0DPA, REP3

value: Uninjured


title: 94T_Micro3,Rhesus Macauqe,12-days SIV infection,acute-infection


title: Adult Fin, IgG, Cut&Tag, 0DPA, REP2


title: 93T_Micro3,Rhesus Macauqe,12-days SIV infection,acute-infection


title: Fin Fold, H3K4me3, Cut&Tag, 24HPF, REP3


title: Adult Fin, IgG, Cut&Tag, 0DPA, REP1


title: Fin Fold, H3K4me3, Cut&Tag, 24HPF, REP2


title: D1063-11_MOLM14_RASi_IL3_Rep1

value: RASi + IL3


title: 93T_Micro1,Rhesus Macauqe,12-days SIV infection,acute-infection


title: 93T_Micro2,Rhesus Macauqe,12-days SIV infection,acute-infection


title: 92T_Micro2,Rhesus Macauqe,control,non-infection


title: Fin Fold, H3K4me3, Cut&Tag, 24HPF, REP1


title: Adult Fin, H3K4me3, Cut&Tag, 0DPA, REP3


title: Adult Fin, H3K4me3, Cut&Tag, 2DPA, REP1


title: Adult Fin, H3K4me3, Cut&Tag, 2DPA, REP2


title: 92T_Micro1,Rhesus Macauqe,control,non-infection


title: Adult Fin, IgG, Cut&Tag, 2DPA, REP2


title: 94T_Micro1,Rhesus Macauqe,12-days SIV infection,acute-infection


title: Adult Fin, H3K4me3, Cut&Tag, 0DPA, REP1


title: Adult Fin, H3K4me3, Cut&Tag, 0DPA, REP2


title: 92T_Micro3,Rhesus Macauqe,control,non-infection


title: Adult Fin, H3K4me3, Cut&Tag, 2DPA, REP3


title: DMSO_P1_H12_S192, Smart-seq2 (multi-omics)

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

description: Smartseq2_mouse_multiomics_processed_TPM.tsv

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7). Statistical analysis was done using R version 4.0.1. We merged the gene expression levels which were calculated by RSEM48 for MGH170 and MGH229 with the ones calculated for the reference samples from Tirosh 2016 (downloaded from https://singlecell.broadinstitute.org/single_cell). Analysis was done mainly using the R package scandal which is freely available at https://github.com/dravishays/scandal.  Gene expression levels were quantified as TPM (transcript-per-million reads).
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics or stained by Ruby (ThermoFisher, V10309) and sorted into 96 well plates. IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
RNA from single cells or single nucleus was first purified with Agencourt RNAClean XP beads (Beckman Coulter). B65Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq sequencer (Illumina). Multi-omics library (DNA methylome and transcriptome) was generated based on the Smart-RRBS protocol (Chaligne et al, 2021).

tag: treatment (idhi)

value: No


title: Control-Replicate 2

library_source: genomic single cell

data_processing:
Libraries were sequenced on a NextSeq 2000 (Illumina) with 50bp read 1, 8bp i7 index read, 16bp i5 index read, and 50bp read 2.  FASTQ files of raw data were processed by Cell Ranger ATAC (10xGenomics, v2.1.0) analysis pipeline. Reads were filtered and aligned to mouse genome mm10 (10xGenomics, refdata-cellranger-arc-mm10-2020-A-2.0.0) using cellranger-atac count() function with default parameters. Then the barcoded and aligned fragment files were loaded by ArchR (version 1.0.1). Low quality cells with minimum TSS enrichment score less than 4 and minimum fragment number less than 1000 were filtered out. Doublets were inferred by addDoubletScores() function and removed using filterDoublets() function with default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated value and text files

extract_protocol:
1ul harsh lysis buffer (50mM Tris (pH=8.0), 5mM EDTA (pH=8.0), 10mM DTT, 1% Tween-20, 1% Triton X-100, 0.1g/l proteinase K, 2.5mM dNTPs, and ERCC Mix (107-fold dilution) and 1ul 10mM barcoded RT primer was added to each well. Plates were incubated at 50°C for 5 mins to lyse cells and proteinase K was heat-inactivated by subsequently incubating at 80°C for 20 mins. To minimize contamination across wells, heavy-duty plate seals and qPCR compression pads (Thermo Fisher Scientific, Cat. 4312639) were used to seal the plates. The lysis reaction was mixed with 2ul reverse transcription master mix 5×buffer (Thermo Fisher Scientific, Cat. 11756500), 2ul 5M Betaine (Sigma-Aldrich, Cat. B0300-1VL), 0.2ul 50mM E5V6NEXT template switch oligo (Integrated DNA Technologies), 0.1ul 200U/ul Maxima H-RT (Thermo Fisher Scientific, Cat. EP0751), 0.1ul 40U/ul NxGen RNase Inhibitor, and 0.6ul nuclease-free water (Thermo Fisher Scientific, Cat. AM9932). The reaction system was then incubated at 42°C for 1.5 hrs, followed by 10 mins at 75°C to inactivate reverse transcriptase. PCR was performed by adding 10ul 2×HiFi PCR mix (Kapa Biosystems, Cat. 7958927001) and 0.5ul 60mM SINGV6 primer and running the following program: 98°C for 3 mins, 20 cycles of 98°C for 20 s, 64°C for 15 s, 72°C for 4 mins, with a final extension step off 5 mins at 72°C.
Mouse embryonic stem cells treated with or without auxin were washed and resuspended in 1xPBS with 0.04% BSA. Nuclei isolation for single-cell ATAC (scATAC) sequencing from cell suspensions was carried out according to the manufacturer’s demonstrated protocol (Demonstrated Protocol, CG000169, Rev E,10xGenomics).  Nuclei were counted using a Luna-II automated cell counter (Logos Biosystems). Approximately 15,000 nuclei per sample were loaded and subjected to the Chromium NextGem scATAC-seq v2 assay (10X Genomics).

tag: strain

value: mESC

value: Control


title: Auxin-Replicate 2

value: Auxin-treated


title: Control-Replicate 1


title: 5 OC-1

type: RNA

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from 5 µM of OC treated for 24 hours

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Clariom_S_Mouse Array. GeneChips were washed and stained in the GeneAtlas® Fluidics Station

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Genes with a linear fold change >1.5 and p-value < 0.05(one-way between-subjects ANOVA) were considered as differentially expressed genes(DEGs). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software.
algorithm: RMA

label: biotin

source_name: cell treated with 5 µM of OC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: B16F10 cells were purchaced from RIKEN and were maintained in RPMI1640

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added to each sample well and then the total RNA sample in 70% ethanol was stored at -20℃ until use.

treatment_protocol: After the 24 hour seeding  in 6-well plates, cells were treated with 0 (Control), 200nM α-MSH (Positive control), and 5µM of OL, and OC for 24 hours

value: murine melanoma cells


title: Auxin-Replicate 1


title: 5 OC-2


title: DMSO_P1_H10_S190, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: OS152, nuclei, m6dA methylated, rep3, 2.2 polymerase

city: San Francisco

value: OS152 cell line

value: metastatic osteosarcoma cell line

value: MYC amplified, CN40

value: m6dA methylated


title: Control_2

description: Gene expression data from meduim treated for 24 hours

source_name: cell treated with meduim


title: 5 OL-2

description: Gene expression data from 5 µM of OL treated for 24 hours

source_name: cell treated with 5 µM of OL


title: alpha-MSH 1

description: Gene expression data from α-MSH treated for 24 hours

source_name: cell treated with 200nM of α-MSH


title: 5 OL-1


title: DMSO_P1_H08_S188, Smart-seq2 (multi-omics)


title: DMSO_P1_H09_S189, Smart-seq2 (multi-omics)


title: P301S_12M-rep3

city: Nan Chong

first: Zhuoze

last: Wu

address: Dongshun Road, Gaoping District

institute: North Sichuan Medical College

description: gene expression in the hippocampus of 12months old P301S mice

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hippocampus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The age-appropriate mice will be sacrificed and their bilateral hippocampus will be separated into a centrifuge tube respectively and frozen in liquid nitrogen.

value: hippocampus

value: p-tau

tag: age


title: P301S_6M-rep3

description: gene expression in the hippocampus of 6months old P301S mice


title: P301S_12M-rep1


title: P301S_6M-rep1


title: C57_12M_rep3

description: gene expression in the hippocampus of 12months old C57 mice


title: C57_12M_rep2


title: P301S_3M-rep3

description: gene expression in the hippocampus of 3months old P301S mice


title: alpha-MSH 2


title: Control_1


title: DMSO_P1_H07_S187, Smart-seq2 (multi-omics)


title: P301S_3M-rep1


title: P301S_12M-rep2


title: DMSO_P1_H03_S183, Smart-seq2 (multi-omics)


title: P301S_3M-rep2


title: P301S_6M-rep2


title: DMSO_P1_G11_S179, Smart-seq2 (multi-omics)


title: DMSO_P1_H11_S191, Smart-seq2 (multi-omics)


title: DMSO_P1_H04_S184, Smart-seq2 (multi-omics)


title: DMSO_P1_G12_S180, Smart-seq2 (multi-omics)


title: DMSO_P1_G09_S177, Smart-seq2 (multi-omics)


title: DMSO_P1_G08_S176, Smart-seq2 (multi-omics)


title: DMSO_P1_G07_S175, Smart-seq2 (multi-omics)


title: C57_6M_rep3

description: gene expression in the hippocampus of 6months old C57 mice


title: C57_12M_rep1


title: C57_6M_rep2


title: C57_3M_rep2

description: gene expression in the hippocampus of 3months old C57 mice


title: DMSO_P1_G06_S174, Smart-seq2 (multi-omics)


title: C57_3M_rep3


title: DMSO_P1_G10_S178, Smart-seq2 (multi-omics)


title: DMSO_P1_G04_S172, Smart-seq2 (multi-omics)


title: DMSO_P1_G03_S171, Smart-seq2 (multi-omics)